Part of the problem is that when KYost took over writing X-23 in the books, they tried to largely write around everything that had been written before (which at the time was NYX and Claremont's early work with her on Uncanny) and start her from scratch. Kyle especially has frequently expressed his desire to retcon NYX out altogether. This is why we've been left with the bit in New X-Men where Logan only PRETENDED he didn't know Laura when they first encountered each other in Uncanny, since according to KYost they met before when she tried to kill him. This is also why her early history is kind of disjointed and mood-swinging. Innocence Lost and Target X were pretty much written to ignore the previous stories.
I think you can make sense of things if you tweak the order of events a bit.
"Canonically" it goes Innocence Lost, Target X, NYX, New X-Men, with Uncanny being dubious (it's been virtually ignored by other writers since).
However if you take this order: Innocence Lost/Facility Flashbacks in Target X > Megan and Debbie > NYX > Laura attacks Logan and is arrested by Cap > New X-Men it works a bit better. Uncanny is still problematic, but I don't think we'll ever be able to fit that end without using VERY broad strokes.
Basically, losing Megan and Debbie is what finally breaks Laura and leads her to the state we find her in when she appears in NYX. Additionally, her state in NYX can be explained by other things we learn about her in later stores: She's quick to form attachments when people show her kindness (IE how she starts latching on to Hellion after he helps defend her against Emma, and later saves her life against Nimrod). She struggles to recognize the difference between choices and orders when presented by authority figures (which is explicitly established as why she joined X-Force: She was mentally and emotionally incapable of recognizing Cyclops offered her a CHOICE. She interpreted it as an order. Logan even calls Scott out on as much). And for much of her life she had no sense of self or self-worth (an ongoing thing, but Liu especially hammered this in). All of these facts make Laura very realistically vulnerable to a manipulative sociopath like Zebra Daddy.
So Daddy swoops in, and uses the carrot to lure her in, perhaps finding her on the streets and giving her a hot meal and a place to stay, before turning the stick against her to gain control (THIS IS EXACTLY HOW MANY WOMEN ARE ENTRAPPED BY TRAFFICKERS IN REAL LIFE). Laura does what she's always done when confronted with an authority figure: She submits. It's not until she connects with Kiden that she finally breaks through, but rather than healing she decides she needs to end everything and goes after Logan.